Nothing
# get otus map
#
# @param nexml nexml object
# @return a list showing the mapping between (internal) otu identifiers and labels (taxonomic names). List is named by the id of the otus block.
# @details largely for internal use
get_otu_maps <- function(nexml){
otus <- as.list(nexml@otus)
names(otus) <- name_by_id(otus)
otu_maps <-
lapply(otus, function(otus){ # loop over all otus nodes
taxon <- sapply(otus@otu, function(otu){ # loop over each otu in the otus set
if(length(otu@label) > 0)
label <- otu@label
else
label <- otu@id
c(otu@id, label)
})
out <- taxon[2, ] #label
names(out) <- taxon[1, ] #id
out
})
otu_maps
}
get_char_maps <- function(nexml){
map <- lapply(nexml@characters, function(characters)
map_chars_to_label(characters@format))
names(map) <- name_by_id(nexml@characters)
map
}
get_state_maps <- function(nexml){
map <- lapply(nexml@characters, function(characters){
if(!isEmpty(characters@format@states))
map_state_to_symbol(characters@format)
else
NULL
})
names(map) <- name_by_id(nexml@characters)
map
}
reverse_map <- function(map){
out <- NULL
if(is.list(map)){
out <- lapply(map,
function(x){
out <- names(x)
names(out) <- x
out})
} else if(is.character(map)) {
out <- names(map)
names(out) <- map
out
}
out
}
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